Taiwan government has initiated several National Priority Science and Technology Programs (NPSTPs) since 1997, namely Hazards Mitigation, Telecommunications, Agricultural Biotechnology, Pharmaceuticals and Biotechnology, Genomic Medicine, Digital Archives, Systems on Chip, Nanotechnology, and e-Learning, through coordinating and integrating R&D resources nationwide. Distinguished from other government-funding R&D projects, they are formed by special institutional arrangements, across different government agencies at cabinet level, and their budgets have first priority to claim. This paper is aimed to analyze the performance of each NPSTP in terms of efficiency.